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Distance education has always served as an option for students who could not attend school in a traditional way. However, educators know very little about online pedagogy and the related use of Web-based Learning Environment (WLE)s as instructional delivery and support systems for education. To make Web-based Instruction (WBI) a good experience, careful attention should be devoted to the elements that comprise the environment: the pedagogical and technical design components. The goal of this study was to investigate the dynamics involved in the HCI that take place within a WLE. The research objective was to examine the existing views of best practice of Web and instructional design by examining the relationship among the look and feel (visual and navigational aspects) of an instructional interface, learning performance of the students, and characteristics of the learner (prior knowledge and experience with computer and Internet, and cognitive styles). To examine the phenomena, the study used a mixed method, and employed a quantitative/qualitative quasi-experimental post-test only design. To test the degree of association among the learner comprehension of interface design, learning performance, and learner characteristics two different levels of an instructional interface were created: with enhancements and without enhancements. After the course enrollment period ended, participants were randomly assigned to the two WLE interfaces. From data analysis, results yielded the following major findings: (a) There was no significant difference in the learning performance means of the participants using the enhanced and nonenhanced interface, (b) a common set of aspects was valued, regardless of the level of the interface, (c) organization, presentation, and usefulness of navigation were identified as equally important elements of the WLE, and screen elements and graphic design were considered equally unimportant, (d) “instruction” was indicated the component that most affected learning performance. Also, no significant differences were found when comparing perceptions of interface usability over time. However, the non-enhanced interface group rated comfort level, clarity, ease in understanding, and organization higher than the enhanced-interface group did. While most of the research supports the relationship between the importance of good principles of Web design and usability and the quality of Web applications, findings of this study revealed that instead of course interface manipulation have improved the learning performance it might have added an extra layer of information for learners to deal with.